I don't see how the author is arriving at this ">99% chance" purely from the numbers provided in the article. Assuming the first (banned IP) seed and the second seed are both in the range 0.4423 - 0.4358 (a stronger assumption than is justified by the example), all this tells us is that the first and second IP addresses both have seeds in a range that would contain 0.4423 - 0.4358 = 0.65% of all Mullvad users, which 0.0065 * 100,000 = 650 users. We've eliminated >99% of users as "suspects", but we haven't actually gotten >99% accuracy in identifying an individual across multiple exit IPs.
In more Bayesian thinking, the overlap in potential seeds is great evidence to think these IP addresses represent one and the same person (or Mullvad VPN account at least), but as far as I can tell, that's not what the author is saying.